The evolution of enzyme function in the isomerases

被引:29
作者
Cuesta, Sergio Martinez [1 ]
Furnham, Nicholas [2 ]
Rahman, Syed Asad [1 ]
Sillitoe, Ian [3 ]
Thornton, Janet M. [1 ]
机构
[1] European Bioinformat Inst EMB LEBI, European Mol Biol Lab, Cambridge CB10 1SD, England
[2] London Sch Hyg & Trop Med, Dept Pathogen Mol Biol, London WC1E 7HT, England
[3] UCL, Div Biosci, Inst Struct & Mol Biol, London WC1E 6BT, England
基金
英国惠康基金;
关键词
DIVERGENT EVOLUTION; CATALYTIC PROMISCUITY; CLASSIFICATION; DISCOVERY; SUPERFAMILIES; CONVERGENCE; PLASTICITY; CONVERSION; DIVERSITY; RACEMASE;
D O I
10.1016/j.sbi.2014.06.002
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.
引用
收藏
页码:121 / 130
页数:10
相关论文
共 61 条
[1]   Toward mechanistic classification of enzyme functions [J].
Almonacid, Daniel E. ;
Babbitt, Patricia C. .
CURRENT OPINION IN CHEMICAL BIOLOGY, 2011, 15 (03) :435-442
[2]   Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function [J].
Almonacid, Daniel E. ;
Yera, Emmanuel R. ;
Mitchell, John B. O. ;
Babbitt, Patricia C. .
PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (03)
[3]   Specificity in Transition State Binding: The Pauling Model Revisited [J].
Amyes, Tina L. ;
Richard, John P. .
BIOCHEMISTRY, 2013, 52 (12) :2021-2035
[4]   Update on activities at the Universal Protein Resource (UniProt) in 2013 [J].
Apweiler, Rolf ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alam-Faruque, Yasmin ;
Alpi, Emanuela ;
Antunes, Ricardo ;
Arganiska, Joanna ;
Casanova, Elisabet Barrera ;
Bely, Benoit ;
Bingley, Mark ;
Bonilla, Carlos ;
Britto, Ramona ;
Bursteinas, Borisas ;
Chan, Wei Mun ;
Chavali, Gayatri ;
Cibrian-Uhalte, Elena ;
Da Silva, Alan ;
De Giorgi, Maurizio ;
Dimmer, Emily ;
Fazzini, Francesco ;
Gane, Paul ;
Fedotov, Alexander ;
Castro, Leyla Garcia ;
Garmiri, Penelope ;
Hatton-Ellis, Emma ;
Hieta, Reija ;
Huntley, Rachael ;
Jacobsen, Julius ;
Jones, Rachel ;
Legge, Duncan ;
Liu, Wudong ;
Luo, Jie ;
MacDougall, Alistair ;
Mutowo, Prudence ;
Nightingale, Andrew ;
Orchard, Sandra ;
Patient, Samuel ;
Pichler, Klemens ;
Poggioli, Diego ;
Pundir, Sangya ;
Pureza, Luis ;
Qi, Guoying ;
Rosanoff, Steven ;
Sawford, Tony ;
Sehra, Harminder ;
Turner, Edward ;
Volynkin, Vladimir ;
Wardell, Tony ;
Watkins, Xavier .
NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D43-D47
[5]   Definitions of enzyme function for the structural genomics era [J].
Babbitt, PC .
CURRENT OPINION IN CHEMICAL BIOLOGY, 2003, 7 (02) :230-237
[6]   The ENZYME database in 2000 [J].
Bairoch, A .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :304-305
[7]   Catalysing new reactions during evolution: Economy of residues and mechanism [J].
Bartlett, GJ ;
Borkakoti, N ;
Thornton, JM .
JOURNAL OF MOLECULAR BIOLOGY, 2003, 331 (04) :829-860
[8]   The generation of new protein functions by the combination of domains [J].
Bashton, Matthew ;
Chothia, Cyrus .
STRUCTURE, 2007, 15 (01) :85-99
[9]   Revealing the hidden functional diversity of an enzyme family [J].
Bastard K. ;
Smith A.A.T. ;
Vergne-Vaxelaire C. ;
Perret A. ;
Zaparucha A. ;
De Melo-Minardi R. ;
Mariage A. ;
Boutard M. ;
Debard A. ;
Lechaplais C. ;
Pelle C. ;
Pellouin V. ;
Perchat N. ;
Petit J.-L. ;
Kreimeyer A. ;
Medigue C. ;
Weissenbach J. ;
Artiguenave F. ;
De Berardinis V. ;
Vallenet D. ;
Salanoubat M. .
Nature Chemical Biology, 2014, 10 (1) :42-49
[10]   The Future of the Protein Data Bank [J].
Berman, Helen M. ;
Kleywegt, Gerard J. ;
Nakamura, Haruki ;
Markley, John L. .
BIOPOLYMERS, 2013, 99 (03) :218-222